On Thu, Sep 27, 2012 at 10:43 PM, Robert Pyle <rpyle@post.harvard.edu>wrote:
> Hi Ralf,
>> I installed scipy from source on Anaconda, reasoning that the dmg was only
> for the python.org installation. I have Apple's latest Xcode, and the
> installation went through without any (apparent) errors.
>> I misspoke when I said I installed 0.11.0rc2; that came with Anaconda CE
> from Continuum.
>
That's good to know, since no changes after 0.11.0rc2 could explain this
issue. Probably just following the Anaconda build method would fix your
segfault.
>> I have also installed 0.11.0 on python.org 2.7.3 from
> scipy-0.11.0-py2.7-python.org-macosx10.6.dmg. This doesn't segfault of
> course, but I do get 9 errors and 9 unknown failures. I'm attaching zipped
> logs for both (verbose=2 for the Anaconda segfault, as you asked). I trust
> the file names are self-explanatory.
>
The errors are due to the beta version of numpy being shipped by Anaconda,
scipy.sparse.csgraph should work as advertised. With numpy 1.7.0 (once
released) those errors should be gone. The single precision failures are
due to Apple's Accelerate Framework, only known solution is to not use it
and compile against ATLAS instead.
Ralf
>>>>> On Sep 27, 2012, at 12:32 PM, Ralf Gommers <ralf.gommers@gmail.com> wrote:
>> >
> >
> > On Thu, Sep 27, 2012 at 4:01 PM, Robert Pyle <rpyle@post.harvard.edu>
> wrote:
> > Hi,
> >
> > I ran into a segfault with AnacondaCE on OSX 10.8.2
> >
> > $ python
> > Python 2.7.3 AnacondaCE (default, Sep 4 2012, 10:42:42)
> > [GCC 4.0.1 (Apple Inc. build 5493)] on darwin
> > Type "help", "copyright", "credits" or "license" for more information.
> > >>> import scipy as sp
> > >>> sp.test()
> > Running unit tests for scipy
> > NumPy version 1.7.0b2
> > NumPy is installed in /opt/anaconda/lib/python2.7/site-packages/numpy
> > SciPy version 0.11.0
> > SciPy is installed in /opt/anaconda/lib/python2.7/site-packages/scipy
> > Python version 2.7.3 AnacondaCE (default, Sep 4 2012, 10:42:42) [GCC
> 4.0.1 (Apple Inc. build 5493)]
> > nose version 1.1.2
> >
> .....................................................................................................................................................................................F.FFFSegmentation
> fault: 11
> >
> > Could you run the tests with "scipy.test(verbose=2) to see where the
> issue occurs?
> >
> >
> > I installed 0.11.0rc2 which seems to run fine for my purposes but where
> scipy.test() gives
> >
> > Did you install both rc2 and final from the dmgs on SourceForge with
> macosx-10.6 in the name?
> >
> > FAILED (KNOWNFAIL=13, SKIP=29, errors=11, failures=73)
> > <nose.result.TextTestResult run=5484 errors=11 failures=73>
> >
> > I attach a zipped file of the error log, in case that's useful.
> >
> > The test errors/failures in that log are all known. The
> IndexError/ValueError ones are because of an issue in numpy 1.7.0b2, which
> should be fixed before the final 1.7.0 release. The other ones are due to
> issues with Apple's Accelerate Framework. So doesn't look related.
> >
> > Can anyone comment on how Anaconda CE was built? I can imagine problems
> could occur if it was built on OS X 10.7 or 10.8 while scipy 0.11.0 was
> built on OS X 10.6.
> >
> > Ralf
> >
> >
> >
> > And a heartfelt thanks to all who work on this. You make my life so
> much easier!
> >
> > Bob Pyle
> > Cambridge, MA
> > _______________________________________________
> > SciPy-User mailing list
> > SciPy-User@scipy.org> > http://mail.scipy.org/mailman/listinfo/scipy-user>>> _______________________________________________
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